More than 60 people are dead and dozens missing after record rainfall caused rivers to burst their banks in Hiroshima and other areas.
The severe weather took many people in southwest Japan by surprise.
Heavy rainfall hammered southern Japan for a third day, prompting new disaster warnings on Kyushu and Shikoku islands on Sunday. Most of the deaths were reported in Hiroshima and Ehime Prefectures, though eight prefectures were impacted.
In neighbouring Okayama prefecture, rescue workers flew in helicopters over areas that are still submerged and otherwise unreachable, looking for signs of life.
"The rescue teams are doing their utmost".
The rain could continue through Sunday, according to the Japan Meteorological Agency.
The assessment of casualties has been hard because of the widespread area affected by the rainfall, flooding and landslides since late last week. Authorities warned that landslides could strike even after rain subsides as the calamity shaped up to be potentially the worst in decades. Landslide warnings were issued in more than a quarter of the nation's prefectures.
Cars travel on roads that have turned to mud.
With the toll mounting, Prime Minister Shinzo Abe cancelled a four-country foreign trip, local media said, and he was expected to visit affected areas later this week.
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A residential area in Okayama prefecture, on the main island of Honshu, was covered in brown water spreading like a huge lake.
Scores of patients‚ some still in their pajamas‚ and nurses were rescued from the isolated Mabi Memorial Hospital in boats rowed by members of Japan's Self Defence Forces.
Video footage showed people being airlifted to hospitals and others heading toward dry land on rafts. They also advised people wait for disaster professionals before venturing into damaged homes because of the dangers of exposed electric lines and hazardous material. "I've been living this town for nearly 70 years, but it was first time to have such heavy rain".
Searches and cleanup efforts were taking place in the southwestern region where several days of heavy rainfall set off flooding and landslides in a widespread area.
"I was in a auto and massive floods of water gushed towards me from the front and back and then engulfed the road".
"We recognize more than 100 cases in which people, including those hit by landslides, are in need of rescue now", Chief Cabinet Secretary Yoshihide Suga told a press conference Saturday.
A man in the far western city of Hiroshima died after falling off a bridge into a river, while a 77-year-old man in Takashima city, Shiga prefecture, was killed after being swept into a canal as he worked to remove debris, NHK said.